Research Topics
| Martin ZachariasSummaryAffiliation: International University Bremen Country: Germany Publications
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Detail Information
Publications
Differential tapasin dependence of MHC class I molecules correlates with conformational changes upon peptide dissociation: a molecular dynamics simulation studyFlorian Sieker
Jacobs University Bremen, Campus Ring 6, 28759 Bremen, Germany
Mol Immunol 45:3714-22. 2008..A possible role of tapasin in case of HLA-B 4402 and other tapasin-dependent alleles could be the stabilization of a peptide-receptive class I conformation...- Minor groove deformability of DNA: a molecular dynamics free energy simulation studyMartin Zacharias
School of Engineering and Science, International University Bremen, D 28759 Bremen, Germany
Biophys J 91:882-91. 2006..The helical parameter analysis of trajectories indicates that an easier partial unstacking of a central TA versus AT basepair step is a likely reason for the larger groove flexibility of the central TATATA case... - Protein-protein docking with a reduced protein model accounting for side-chain flexibilityMartin Zacharias
Computational Biology, School of Engineering and Science, International University Bremen, 28759 Bremen, Germany
Protein Sci 12:1271-82. 2003..The approach could be extended to include protein loop flexibility, and might also be useful for docking of modeled protein structures... - Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBPMartin Zacharias
Computational Biology, School of Engineering and Science, International University Bremen, Bremen, Germany
Proteins 54:759-67. 2004..The approach could provide a computationally efficient way to approximately account for receptor flexibility during docking of large numbers of putative ligands and putative docking geometries... - Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation studyMartin Zacharias
International University Bremen, School of Engineering and Science, D 28759 Bremen, Germany
Biophys J 87:2203-14. 2004..In particular binding of the peptide C-terminus may require conformational stabilization by chaperone proteins during peptide loading... - ATTRACT: protein-protein docking in CAPRI using a reduced protein modelMartin Zacharias
International University Bremen, Computational Biology, School of Engineering and Science, Bremen, Germany
Proteins 60:252-6. 2005..These conformational changes not accounted for during docking are a likely reason for the unrealistic predictions in 2 cases (Targets 9 and 18)... - Influence of a fluorobenzene nucleobase analogue on the conformational flexibility of RNA studied by molecular dynamics simulationsMartin Zacharias
International University Bremen, School of Engineering and Science, D 28759 Bremen, Germany
Nucleic Acids Res 32:6304-11. 2004..Instead, the conformational fluctuations of the base analogues lead to an enhanced accessibility of the bases in the major and minor grooves of the helix compared with a regular base pair... - Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibilityAndreas May
School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
Proteins 69:774-80. 2007..Possible improvements of the docking approach in particular at the scoring and refinement steps are discussed... - Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation studyDanilo Roccatano
School of Engineering and Science, International University Bremen, Campus Ring 1, D 28759, Bremen, Germany
Biopolymers 83:467-76. 2006..The absence of the phenyl ring in F87A mutant promotes interactions of the DMSO molecule with the heme iron resulting in water displacement by DMSO at the catalytic heme center... - PTools: an opensource molecular docking libraryAdrien Saladin
Computational Biology, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
BMC Struct Biol 9:27. 2009..Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application... - Prediction of protein-protein interaction sites using electrostatic desolvation profilesSebastien Fiorucci
School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
Biophys J 98:1921-30. 2010..Applications to several antigen-antibody complexes demonstrated that the approach might be useful not only to predict protein interaction sites in general but to map potential antigenic epitopes on protein surfaces... - Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulationsRanjit P Bahadur
School of Engineering and Science, Jacobs University Bremen, Bremen, Germany
Biophys J 97:3139-49. 2009..It indicates that electrostatic interactions near RNA molecules can lead to a shift in the equilibrium toward the bound form of an interacting partner before it enters the binding pocket... - Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein dockingAndreas May
School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
Proteins 70:794-809. 2008..This result indicates that inclusion of global flexibility can facilitate in silico protein-protein association such that a greater number of different start configurations results in favorable complex formation... - Dissecting protein-RNA recognition sitesRanjit Prasad Bahadur
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany
Nucleic Acids Res 36:2705-16. 2008..The 2'OH is a major player in protein-RNA recognition, and shape complementarity an important determinant, whereas electrostatics and direct base-protein interactions play a lesser part than in protein-DNA recognition... - Accounting for loop flexibility during protein-protein dockingKarine Bastard
Computational Biology, School of Engineering and Science, International University Bremen, Bremen, Germany
Proteins 62:956-69. 2006..We also show that introducing loop flexibility on the isolated protein form during systematic docking largely improves the predictions of relative position of the partners in comparison with rigid-body docking... - Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling methodSrinivasaraghavan Kannan
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany
J Struct Biol 166:288-94. 2009..The approach is well suited for applications in structure refinement and for systematic force field improvement... - Temperature dependence of looping rates in a short peptideDanilo Roccatano
School of Engineering and Science, Jacobs University of Bremen, Campus Ring 1, D 28759, Bremen, Germany
J Phys Chem B 111:2639-46. 2007..5 x 10(8) s(-1) at 280 K to 8.2 x 10(8) s(-1) at 340 K in H2O, which was about four times larger than the experimental data. The calculated activation parameters were Ea = 24.7 +/- 1.5 kJ mol(-1) and ln(A/s(-1)) = 29.4 +/- 0.1 in H2O... - Local and global effects of strong DNA bending induced during molecular dynamics simulationsJeremy Curuksu
Computational Biology, School of Engineering and Science, Jacobs University, Campus Ring 1, D 28759 Bremen, Germany
Nucleic Acids Res 37:3766-73. 2009..Both these observations suggest that DNA is mechanically more complex than simple elastic rod models would imply... - Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I allelesFlorian Sieker
School of Engineering and Science, International University Bremen, D 28759 Bremen, Germany
Protein Sci 16:299-308. 2007..A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles... - Refinement of protein cores and protein-peptide interfaces using a potential scaling approachRalph Nico Riemann
International University Bremen, School of Engineering and Science, D-28759 Bremen, Germany
Protein Eng Des Sel 18:465-76. 2005..Depending on the accuracy of the protein main chain, it also gives significantly better results compared with the standard rotamer search method... - Peptide binding to MHC class I and II proteins: new avenues from new methodsRakina Yaneva
Biochemistry and Cell Biology, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
Mol Immunol 47:649-57. 2010..Here, we review these recent achievements and suggest avenues for further work... - Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solventSrinivasaraghavan Kannan
School of Engineering and Science, Jacobs University Bremen, Bremen D 28759, Germany
Proteins 78:2809-19. 2010.... - Accounting for global protein deformability during protein-protein and protein-ligand dockingAndreas May
Computational Biology, School of Engineering and Science, International University Bremen, Campus Ring 6, D-28759 Bremen, Germany
Biochim Biophys Acta 1754:225-31. 2005..Accounting for receptor conformational changes in pre-calculated global degrees of freedom might offer a promising route to improve systematic docking screening simulations... - Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: a molecular dynamics simulation studyRakina Yaneva
School of Engineering and Science, Jacobs University Bremen, Campus Ring 6, D 28759 Bremen, Germany
Biopolymers 91:14-27. 2009.... - Prediction of antigenic epitopes on protein surfaces by consensus scoringShide Liang
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany
BMC Bioinformatics 10:302. 2009..Only a few structure-based epitope prediction algorithms are available and they have not yet shown satisfying performance... - Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulationDanilo Roccatano
School of Engineering and Science, International University Bremen, Campus Ring 1, D 28759 Bremen, Germany
Biopolymers 85:407-21. 2007..The simulations indicate that the rapid conformational changes of the tails can modulate the DNA accessibility within a few nanoseconds... - Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potentialSrinivasaraghavan Kannan
School of Engineering and Science, International University Bremen, D 28759 Bremen, Germany
Proteins 66:697-706. 2007.... - Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulationsSrinivasaraghavan Kannan
Jacobs University Bremen, D 28759 Bremen, Germany
Phys Chem Chem Phys 11:10589-95. 2009..5) kcal mol(-1) and enthalpy change of approximately -37 kcal mol(-1) for (dCGCG)(2) duplex formation was in good agreement with corresponding experimental values of approximately -3.9 kcal mol(-1) and -38.5 kcal mol(-1), respectively... - B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulationsSrinivasaraghavan Kannan
School of Engineering and Science, International University Bremen, Bremen, Germany
Biophys J 91:2956-65. 2006..Severe untwisting of DNA below an average of 25 degrees per basepair step resulted in the onset of a global structural transition with a significantly smaller twist at one end of the DNA compared to the other... - Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross dockingAndreas May
School of Engineering and Science, Jacobs University Bremen, Campus Ring 6, D 28759 Bremen, Germany
J Med Chem 51:3499-506. 2008..The inclusion of only the soft collective degrees of freedom during docking resulted in improved docking performance at a very modest increase (doubling) of the computational demand... - A statistical analysis of random mutagenesis methods used for directed protein evolutionTuck Seng Wong
International University Bremen (IUB, Campus Ring 8, 28759 Bremen, Germany
J Mol Biol 355:858-71. 2006..5% are amino acids with chemically different side-chains. Statistical information for each mutagenesis method can further be used to investigate the mutational spectra in protein regions regarded as important for the property of interest... - Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulationsJeremy Curuksu
Computational Biology, School of Engineering and Science, Jacobs University, Bremen, Germany
Biophys J 97:2004-13. 2009..The range of free-energy changes associated with kt38 opening and unwinding are compatible with the idea that K-turns may facilitate biologically relevant motions during large-scale ribosome dynamics... - Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulationsSrinivasaraghavan Kannan
School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
Biophys J 93:3218-28. 2007..Such conformations may correspond to long-lived trapped states that have been postulated to account for the folding kinetics of nucleic acid hairpins that are slower than expected for a semiflexible polymer of the same size... - Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I moleculesFlorian Sieker
School of Engineering and Science, Jacobs University Bremen, D 28759 Bremen, Germany
Curr Protein Pept Sci 10:286-96. 2009..In addition, structure based approaches to predict class I binding specificity including molecular modeling and molecular dynamics (MD) simulations will also be presented... - Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approachJeremy Curuksu
School of Engineering and Science, Jacobs University, Campus Ring 1, D 28759 Bremen, Germany
J Chem Phys 130:104110. 2009..It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules... - Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sitesJeremy Curuksu
School of Engineering and Science, Jacobs University, Campus Ring 1, D 28759 Bremen, Germany
Nucleic Acids Res 36:2268-83. 2008.... - Tapasin dependence of major histocompatibility complex class I molecules correlates with their conformational flexibilityMalgorzata Anna Garstka
Molecular Life Science, Jacobs University Bremen, Bremen, Germany
FASEB J 25:3989-98. 2011..MD simulations are a useful tool to predict such conformational disorder of class I molecules... - Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixtureDanilo Roccatano
School of Engineering and Science, International University Bremen, Campus Ring 1, D 28725, Bremen, Germany
Biopolymers 78:259-67. 2005..During the simulation, no DMSO molecule penetrated the active site. However, a significant accumulation of DMSO molecules close to the substrate-binding site and to the Flavin Mononucleotide (FMN) reductase domain interface was observed... - Effect of hexafluoroisopropanol alcohol on the structure of melittin: a molecular dynamics simulation studyDanilo Roccatano
School of Engineering and Science, International University of Bremen, Campus Ring 1, D 28725 Bremen, Germany
Protein Sci 14:2582-9. 2005..Finally, a stabilizing effect promoted by the presence of counter-ions was also observed in the simulations... - Distance distributions of short polypeptides recovered by fluorescence resonance energy transfer in the 10 A domainHarekrushna Sahoo
School of Engineering and Science, International University Bremen, Campus Ring 1, D-28759 Bremen, Germany
J Am Chem Soc 128:8118-9. 2006..10%) of the conformations are already in van der Waals contact when excitation occurs... - Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica-Exchange Molecular Dynamics SimulationsSrinivasaraghavan Kannan
School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D 28759 Bremen, Germany
Int J Mol Sci 10:1121-37. 2009..Folding does not introduce any significant sterical strain as reflected by similar energy distributions of bonded energy terms (bond length, bond angle and dihedral angle) of folded and unfolded Trp-cage structures... - Tapasin and other chaperones: models of the MHC class I loading complexCynthia Anne Wright
Biochemistry and Cell Biology, International University Bremen, D-28759 Bremen, Germany
Biol Chem 385:763-78. 2004..It introduces new models for the mode of action of tapasin, the role of the class I loading complex in peptide editing, and the intracellular localization of class I molecules... - Sequence context dependence of tandem guanine:adenine mismatch conformations in RNA: a continuum solvent analysisGilberto Villescas-Diaz
Theoretische Biophysik, , Jena, Germany
Biophys J 85:416-25. 2003..Electrostatic contributions are predicted to make the most significant contribution to the sequence context dependence on the structural preference of tG:A mismatches... - Enzymatic degradation of beta- and mixed alpha,beta-oligopeptidesTobias Heck
Eawag, Swiss Federal Institute of Aquatic Science and Technology,
Chem Biodivers 3:1325-48. 2006..Astonishingly, DmpA exhibited much higher catalytical rates for the mixed dipeptide carnosine (H-betahGly-His-OH) than for any other substrate described until now... - The human T-cell lymphotropic virus type-I dimerization initiation site forms a hairpin loop, unlike previously characterized retroviral dimerization motifsTom P Monie
Department of Medicine, University of Cambridge, Level 5, Addenbrooke's Hospital, UK
Biochemistry 43:6085-90. 2004..Molecular modeling demonstrates that this can be formed by an unusual C:synG base pair closing the loop. Comparative phylogeny indicates that such a motif may also exist in other deltaretroviruses... - Design and biological evaluation of linear and cyclic phosphopeptide ligands of the N-terminal SH2 domain of protein tyrosine phosphatase SHP-1Diana Imhof
Institute of Biochemistry and Biophysics, Biological and Pharmaceutical Faculty, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
J Med Chem 48:1528-39. 2005..They partially competed with Ros pY2267 in the activation assay. Such cyclic structures may serve as scaffolds for competitive SHP-1 inhibitor design targeting N-SH2 domain-protein interactions that block SHP-1 activation... - A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNAYvonne Ihle
Molekulare Biophysik NMR Spektroskopie, , D 07745 Jena, Germany
Nucleic Acids Res 33:2003-11. 2005..Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence... - Molecular dynamics simulations on the free and complexed N-terminal SH2 domain of SHP-2Karin Wieligmann
Theoretische Biophysik, , Beutenbergstr. 11, D-07745 Jena, Germany
In Silico Biol 2:305-11. 2002..The results support a mechanism of signal transduction where SH2-peptide binding modulates the domain flexibility and reduces its capacity to fit into the entrance of the PTP catalytic domain of SHP-2... - Sequence specificity of SHP-1 and SHP-2 Src homology 2 domains. Critical roles of residues beyond the pY+3 positionDiana Imhof
Department of Chemistry, Ohio State University, Columbus, Ohio 43210, USA
J Biol Chem 281:20271-82. 2006..Examination of pY motifs from known SHP-1 and SHP-2-binding proteins shows that many of the pY motifs contain a hydrophobic or positively charged residue(s) at the pY+4 and pY+5 positions... - Phosphopeptide ligands of the SHP-1 N-SH2 domain: effects on binding and stimulation of phosphatase activityKornelia Hampel
Institute of Biochemistry and Biophysics, Biological and Pharmaceutical Faculty, Friedrich Schiller University, Philosophenweg 12, 07743 Jena, Germany
ChemMedChem 1:869-77. 2006..Therefore, their binding does not force the conformational transition necessary to trigger the dissociation of N-SH2 and the catalytic domain... - Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomesMatthias Homann
Institute of Microbiology and Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, D 64287 Darmstadt, Germany
Comb Chem High Throughput Screen 9:491-9. 2006..We demonstrate that antigen-tagged preparations of the aptamer can bind to live trypanosomes and that they can be used to re-direct immunoglobulins to the parasite surface... - Maturation of the 5S rRNA 5' end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcaniiAnnette Hölzle
Molekulare Botanik, Universitat Ulm, 89069 Ulm, Germany
RNA 14:928-37. 2008..Knock out of the tRNase Z gene in Haloferax volcanii is lethal, showing that the protein is essential for the cell... - TbMP42 is a structure-sensitive ribonuclease that likely follows a metal ion catalysis mechanismMoritz Niemann
Genetics, Darmstadt University of Technology, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
Nucleic Acids Res 36:4465-73. 2008..Together, the data are suggestive of a Zn(2+)-dependent metal ion catalysis mechanism for the ribonucleolytic activity of rTbMP42...